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1.05 A Crystal Structure of D30A Mutant of Nitrophorin 4 from Rhodnius Prolixus Complexed with Nitric Oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KOI PDB entry 1KOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Ammonium Phosphate 3.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.358 α = 90 b = 42.839 β = 94.14 c = 53.077 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 Bent conical Si-mirror (Rh coating) 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.05 21.9 97.9 0.059 0.059 12.3 2.98 71942 71942 6.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.09 99.4 0.259 0.259 2.2 2.15 7226
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1KOI 1.05 16.24 71942 67153 3571 96.29 0.15354 0.15354 0.15221 0.1568 0.17857 0.1602 RANDOM 8.166
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.423 r_dihedral_angle_1_deg 7.418 r_sphericity_bonded 4.66 r_scangle_it 4.541 r_scbond_it 3.308 r_mcangle_it 2.736 r_mcbond_it 1.975 r_rigid_bond_restr 1.944 r_angle_refined_deg 1.59 r_angle_other_deg 0.727
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 7.423 r_dihedral_angle_1_deg 7.418 r_sphericity_bonded 4.66 r_scangle_it 4.541 r_scbond_it 3.308 r_mcangle_it 2.736 r_mcbond_it 1.975 r_rigid_bond_restr 1.944 r_angle_refined_deg 1.59 r_angle_other_deg 0.727 r_metal_ion_refined 0.311 r_nbd_other 0.278 r_symmetry_vdw_other 0.265 r_nbd_refined 0.249 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.118 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1425 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data reduction d*TREK data scaling